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Showing :
phyloseq
•
reset
2
votes
9
replies
19k
views
Error in file(con, “r”) : cannot open the connection
r
phyloseq
import_biom
otu
qiime
updated 8.5 years ago by
mcmurdie
▴ 20 • written 8.5 years ago by
moanam
• 0
0
votes
5
replies
6.2k
views
Problems with installation of 'phyloseq
phyloseq
updated 2.7 years ago by
Kevin Blighe
★ 3.9k • written 2.7 years ago by
Ina
• 0
2
votes
2
replies
6.2k
views
Interpretation of intercept-only model (~1) in DESeq2
deseq2
phyloseq
updated 8.1 years ago by
Michael Love
41k • written 8.1 years ago by
piensaglobalmente
▴ 10
1
vote
8
replies
5.7k
views
Cannot read Biom file
r
biomformat
phyloseq
updated 6.4 years ago by
Axel Klenk
▴ 990 • written 6.4 years ago by
channen1221
• 0
0
votes
1
reply
4.4k
views
Phyloseq: How to add sample table to phyloseq object
phyloseq
sample_table
phyloseq
9.2 years ago
Brian Smith
▴ 120
1
vote
1
reply
3.5k
views
Setting up bioconductor on a Linux server using conda
dada2
conda
phyloseq
updated 3.0 years ago by
James W. MacDonald
65k • written 3.0 years ago by
Daniel
• 0
1
vote
1
reply
3.4k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome
normalization
variancestabilizingtransformation
phyloseq
7.0 years ago
stats134711
• 0
3
votes
2
replies
3.2k
views
DESeq2 iterative size factor normalization did not converge
deseq2
microbiome
phyloseq
updated 6.6 years ago by
Michael Love
41k • written 6.6 years ago by
couchc
• 0
0
votes
6
replies
3.1k
views
Alpha diversity on Rlogtransformed data
deseq2
phyloseq
metagenomeseq
8.3 years ago
David
▴ 860
0
votes
2
replies
2.8k
views
Problems with bioconductor after updating R to 3.6.2
R 3.6.2 update problems with igraph and phangorn update
Phyloseq
igraph
phangorn
Tutorial
updated 4.3 years ago by
Martin Morgan
25k • written 4.3 years ago by
crgarcia
• 0
5
votes
11
replies
2.7k
views
Error while installing Phyloseq using biocLite
bioclite
phyloseq
install error
5.5 years ago
khp
▴ 30
0
votes
9
replies
2.4k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2
phyloseq
5.5 years ago
eoin
• 0
1
vote
1
reply
2.2k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq
Phylogenetics
updated 12 months ago by
RMiller
▴ 10 • written 12 months ago by
kevin
• 0
1
vote
10
replies
2.2k
views
Multi-factor Comparison in DESeq 2 Issue
deseq2
phyloseq
updated 9.1 years ago by
Ryan C. Thompson
★ 7.9k • written 9.1 years ago by
locon833
• 0
1
vote
2
replies
2.2k
views
Bioconductor install error
phyloseq
Bioconductor
3.3 years ago
Tess
• 0
0
votes
1
reply
2.2k
views
phyloseq merge_samples attempt to set rownames on an object with no dimensions
phyloseq
merge_samples
rownames
error
7.5 years ago
newmanss
• 0
1
vote
2
replies
2.1k
views
DESeqs two-factor two-level, interaction is interested
Sequencing
GO
phyloseq
DESeq2
Sequencing
GO
phyloseq
DESeq2
updated 9.8 years ago by
Michael Love
41k • written 9.8 years ago by
Shucong Li
▴ 60
3
votes
2
replies
2.1k
views
DESEQ2 (R) design/contrast formula questions
deseq2
phyloseq
multiple factor design
paired samples
updated 8.0 years ago by
mcmurdie
▴ 20 • written 8.0 years ago by
pete_bioinfo
▴ 10
0
votes
1
reply
2.1k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3
Metagenomics
phyloseq
updated 2.8 years ago by
Levi Waldron
★ 1.1k • written 2.8 years ago by
Saraswati
• 0
0
votes
1
reply
2.0k
views
ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree
ggplot2
phyloseq
geom_boxplot
facet_plot
updated 7.1 years ago by
Guangchuang Yu
★ 1.2k • written 7.1 years ago by
matthew.wipperman
• 0
0
votes
1
reply
2.0k
views
Error with phyloseq R package with Conda install
software error
phyloseq
anaconda
written 7.4 years ago by
kpitz23
• 0
0
votes
3
replies
1.9k
views
Newer version of DESeq2 gives different results
deseq2
phyloseq
updated 7.8 years ago by
Michael Love
41k • written 7.8 years ago by
am39
• 0
0
votes
1
reply
1.9k
views
phyloseq biom json format conversion needed to hdf5 format for qiime
biom
json
hdf5
qiime
phyloseq
updated 7.4 years ago by
Bernd Fischer
▴ 550 • written 7.4 years ago by
newmanss
• 0
1
vote
3
replies
1.9k
views
Error bars on DESeq2 visuals
deseq2
metagenomics
phyloseq
ggplot2
6.6 years ago
lauren.czaplicki
• 0
2
votes
1
reply
1.9k
views
Using DESeq2 after agglomerating OTUs
phyloseq
deseq2
estimatesizefactors
updated 8.3 years ago by
Michael Love
41k • written 8.3 years ago by
brandilyn.peters
• 0
0
votes
2
replies
1.8k
views
Error in taxa_are_rows(x) : trying to get slot "taxa_are_rows" from an object (class "otu_table") that is not an S4 object
deseq2
phyloseq
3.7 years ago
jaiber.solano.i
• 0
0
votes
2
replies
1.8k
views
Controlling colours assigned to order in DeSeq2 plot in phyloseq
phyloseq
color
ggplot2
updated 7.1 years ago by
Michael Love
41k • written 7.1 years ago by
sarahmacdonald86
• 0
0
votes
4
replies
1.7k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings
phyloseq
updated 2.0 years ago by
James W. MacDonald
65k • written 2.0 years ago by
Eman
• 0
0
votes
4
replies
1.7k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData
phyloseq
dada2
2.2 years ago
ymtan
• 0
0
votes
1
reply
1.6k
views
Install package phyloseq
installation
phyloseq
updated 6.0 years ago by
Martin Morgan
25k • written 6.0 years ago by
layeb
• 0
0
votes
3
replies
1.6k
views
I cannot install "microbiome"
GenomeInfoDbData
microbiome
phyloseq
updated 19 months ago by
Marcel Ramos
690 • written 19 months ago by
kikiki
• 0
0
votes
3
replies
1.5k
views
DESeq2 blocking by condition over time
deseq2
phyloseq
time course
7.6 years ago
akp
• 0
0
votes
1
reply
1.5k
views
tip_glom and annotations?
ggtree
treeio
phyloseq
annotation
tip_glom
updated 6.1 years ago by
Guangchuang Yu
★ 1.2k • written 6.1 years ago by
werdnus
• 0
0
votes
1
reply
1.5k
views
Import_biom with tree problem
phyloseq
mothur
16s
5.4 years ago
andrebolerbarros
▴ 20
0
votes
1
reply
1.5k
views
Phyloseq to DESeq2 with multiple variables
deseq2
phyloseq
multiple time points
updated 6.7 years ago by
Michael Love
41k • written 6.7 years ago by
campbell87
• 0
2
votes
2
replies
1.5k
views
Bioconductor phyloseq taking forever to install?
Bioconductor
phyloseq
3.4 years ago
garfield320
▴ 30
0
votes
0
replies
1.5k
views
Loading Phyloseq into R- R crashes
software error
phyloseq
R
9.2 years ago
locon833
• 0
2
votes
2
replies
1.4k
views
DESeq2 in phyloseq
deseq2
phyloseq
7.1 years ago
sarahmacdonald86
• 0
1
vote
2
replies
1.4k
views
rlogTransformation vs getVarianceStabilizedData
deseq2
r
phyloseq
updated 7.3 years ago by
Michael Love
41k • written 7.3 years ago by
fabian.roger08
▴ 10
1
vote
1
reply
1.3k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2
R
microbiome
phyloseq
qiime
updated 6.3 years ago by
Michael Love
41k • written 6.3 years ago by
ssingh59
• 0
0
votes
1
reply
1.3k
views
phyloseq - plot_bar() error
phyloseq
plot_bar()
updated 8.4 years ago by
mcmurdie
▴ 20 • written 8.4 years ago by
Brian Smith
▴ 120
0
votes
6
replies
1.3k
views
convert default phylip to sequential phylip
phyloseq
Phylogenetics
updated 11 months ago by
yrkkhdesiserials
• 0 • written 2.6 years ago by
memy
• 0
0
votes
1
reply
1.3k
views
DESeqs two-factor two-level, interaction is interested
Sequencing
GO
phyloseq
DESeq2
Sequencing
GO
phyloseq
DESeq2
9.7 years ago
Shucong Li
▴ 60
0
votes
0
replies
1.3k
views
How to pool phyloseq data?
phyloseq
r
updated 2.0 years ago by
Michael Love
41k • written 2.0 years ago by
strep
• 0
0
votes
1
reply
1.3k
views
phyloseq heatmap blank after multiple package updates
phyloseq
heatmap
updated 6.6 years ago by
Wolfgang Huber
★ 13k • written 6.6 years ago by
newmanss
• 0
0
votes
0
replies
1.3k
views
Phylogenetic tree from marker genes
ape
phyloseq
dist
metagenomics
6.9 years ago
David
▴ 860
0
votes
0
replies
1.2k
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq
installation
ade4
macos
6.4 years ago
sprague
• 0
0
votes
0
replies
1.2k
views
Phyloseq/DEseq transformed data
DESeq
phyloseq
DESeq
phyloseq
10.0 years ago
Susan Holmes
▴ 120
4
votes
3
replies
1.1k
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2
phyloseq
updated 3.1 years ago by
Michael Love
41k • written 3.1 years ago by
trichorico
▴ 10
0
votes
1
reply
1.1k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics
deseq2
PHYLOSEQ
updated 3.7 years ago by
Michael Love
41k • written 3.7 years ago by
dc
• 0
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